Is lower clearance/higher clearance by itself change the cost of making a car, or not? Not only BMW but in other brands, it seems cars with lower clearance are sold at lower prices than a similarly equipped car with higher clearance. I want to understand why.

It's not that manufacturers have to charge more for a lifted version, but rather that they can charge more. Crossovers and SUV's have a greater perceived value than wagons and hatches. It's no coincidence that other manufacturers have followed the Subaru Outback formula for greater profits. The new allroad costs about $3k more than the Avant wagon on which it's based. The traditional wagon is nearly dead in the US, and it's no secret why that is.